This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Numerous large multidimensional datasets communicating the relationships between individual proteins and protein superfamilies have been collected by experimental means. Extracting relevant information from these datasets through qualitative and quantitative analysis has proven difficult. Cytoscape, an open source Web-based application developed for the purposes of visualizing and analyzing protein-protein networks, could serve as a useful tool for studying these datasets. Our goal is to develop new "plug-ins" for Cytoscape that will allow researchers to visually and quantitatively understand experimentally determined associations between protein superfamilies. Potentially, we would like to couple Cytoscape with structural analysis software to provide even more powerful means of investigating large protein superfamily datasets.